Examples with StageExecutorResult pipelite.stage.executor.StageExecutorResult used on opensource projects

Example 26 with StageExecutorResult

use of pipelite.stage.executor.StageExecutorResult in project pipelite by enasequence.

the class AbstractAsyncExecutor method poll.

private void poll(StageExecutorRequest request, StageExecutorResultCallback resultCallback) {
    try {
        StageExecutorResult result = poll(request);
        if (result.isSubmitted()) {
            result = StageExecutorResult.internalError(new PipeliteException("Unexpected state during asynchronous poll: " + result.getExecutorState().name()));
        }
        resultCallback.accept(result);
    } catch (Exception ex) {
        StageExecutorResult result = StageExecutorResult.internalError(ex);
        resultCallback.accept(result);
    }
}

Example 27 with StageExecutorResult

use of pipelite.stage.executor.StageExecutorResult in project pipelite by enasequence.

the class AbstractLsfExecutor method submit.

@Override
protected SubmitResult submit(StageExecutorRequest request) {
    outFile = getExecutorParams().resolveLogFile(request, LsfFilePathResolver.Format.WITHOUT_LSF_PATTERN);
    StageExecutorResult result = RetryTask.DEFAULT.execute(r -> getCmdRunner().execute(getSubmitCmd(request)));
    String jobId = null;
    if (!result.isError()) {
        jobId = extractSubmittedJobIdFromBsubOutput(result.getStageLog());
        logContext(log.atInfo(), request).log("Submitted LSF job " + jobId);
        result.setSubmitted();
    }
    return new SubmitResult(jobId, result);
}

Example 28 with StageExecutorResult

use of pipelite.stage.executor.StageExecutorResult in project pipelite by enasequence.

the class AbstractLsfExecutor method extractResultFromBjobsOutput.

/**
 * Extracts job result from a single line of bjobs output.
 */
public static JobResult extractResultFromBjobsOutput(String str) {
    String[] column = str.split("\\|");
    if (column.length != 7) {
        log.atWarning().log("Unexpected bjobs output line: " + str);
        return null;
    }
    StageExecutorResult result;
    if (column[BJOBS_COLUMN_STATUS].equals(BJOBS_STATUS_DONE)) {
        result = StageExecutorResult.success();
        result.addAttribute(StageExecutorResultAttribute.EXIT_CODE, String.valueOf(0));
    } else if (column[BJOBS_COLUMN_STATUS].equals(BJOBS_STATUS_EXIT)) {
        result = StageExecutorResult.error();
        result.addAttribute(StageExecutorResultAttribute.EXIT_CODE, String.valueOf(column[BJOBS_COLUMN_EXIT_CODE]));
    } else {
        result = StageExecutorResult.active();
    }
    String jobId = column[BJOBS_COLUMN_JOB_ID];
    result.addAttribute(StageExecutorResultAttribute.JOB_ID, jobId);
    if (result.isSuccess() || result.isError()) {
        result.addAttribute(StageExecutorResultAttribute.EXEC_HOST, column[BJOBS_COLUMN_HOST]);
        result.addAttribute(StageExecutorResultAttribute.CPU_TIME, column[BJOBS_COLUMN_CPU_TIME]);
        result.addAttribute(StageExecutorResultAttribute.MAX_MEM, column[BJOBS_COLUMN_MAX_MEM]);
        result.addAttribute(StageExecutorResultAttribute.AVG_MEM, column[BJOBS_COLUMN_AVG_MEM]);
    }
    JobResult jobResult = new JobResult();
    jobResult.jobId = jobId;
    jobResult.result = result;
    return jobResult;
}

Example 29 with StageExecutorResult

use of pipelite.stage.executor.StageExecutorResult in project pipelite by enasequence.

the class AbstractLsfExecutor method bjobs.

private static String bjobs(CmdRunner cmdRunner, List<String> jobIds) {
    String str = String.join(" ", jobIds);
    log.atFine().log("Checking LSF job results using bjobs: " + str);
    // Ignore exit code as bjobs returns 255 if some of the jobs are not found.
    StageExecutorResult result = cmdRunner.execute(BJOBS_CMD + str);
    return result.getStageLog();
}

Example 30 with StageExecutorResult

use of pipelite.stage.executor.StageExecutorResult in project pipelite by enasequence.

the class AbstractLsfExecutor method extractResultFromBhistOutputOrOutFile.

/**
 * Extracts stage execution result from bhist output or out file. Returns null if the result could
 * not be extracted.
 */
public static StageExecutorResult extractResultFromBhistOutputOrOutFile(String str) {
    if (str == null) {
        return null;
    }
    if (// bhist -f result
    str.contains("Done successfully") || // output file result
    str.contains("Successfully completed")) {
        StageExecutorResult result = StageExecutorResult.success();
        result.addAttribute(StageExecutorResultAttribute.EXIT_CODE, "0");
        return result;
    }
    Integer exitCode = extractExitCodeFromBhistOutputOrOutFile(str);
    if (exitCode != null) {
        StageExecutorResult result = StageExecutorResult.error();
        result.addAttribute(StageExecutorResultAttribute.EXIT_CODE, String.valueOf(exitCode));
        return result;
    }
    return null;
}